Potential Geographic Range of the Endangered Reed Parrotbill Paradoxornis heudei under Climate Change.

The phenomenon of global climate change can impact the geographic range and biodiversity, thereby heightening the vulnerability of rare species to extinction. The reed parrotbill (Paradoxornis heudei David, 1872) is endemic to central and eastern China, it is mainly distributed in the middle and lower reaches of the Yangtze River Plain and the Northeast Plain. In this study, eight of ten algorithms of the species distribution model (SDM) were used to evaluate the impact of climate change on the potential distribution of P. heudei under current and future climate scenarios and to analyze the possible related climate factors. After checking the collected data, 97 occurrence records of P. heudei were used. The relative contribution rate shows that among the selected climatic variables, temperature annual range (bio7), annual precipitation (bio12), and isothermality (bio3) were the principal climatic factors to limit the habitat suitability of P. heudei. The suitable habitat for P. heudei is primarily concentrated in the central-eastern and northeast plains of China, particularly in the eastern coastal region, spanning a mere area of 57,841 km2. The habitat suitability of P. heudei under different representative concentration pathway (RCP) scenarios was predicted to be different under future climatic conditions, but all of them had a larger range than the current one. The species distribution range could expand by more than 100% on average compared with the current range under the four scenarios in 2050, while it could contract by approximately 30% on average relative to the 2050 range in 2070 under different climate change scenarios. In the future, northeastern China may serve as a potential suitable habitat for P. heudei. The changes in the spatial and temporal distributions of P. heudei's range are of utmost importance in identifying high-priority conservation regions and devising effective management strategies for its preservation.

Using DNA barcoding and field surveys to guide wildlife management at Nanjing Lukou International Airport, China.

The conflicts between wildlife and aircraft have increased due to the development of the aviation industry. While many studies have quantified the relative hazards of wildlife to aircraft, few studies have combined DNA barcoding techniques with field surveys of bird communities in different habitats to reveal the exact species involved in bird strikes and how the habitat heterogeneity around airports affects bird communities and even the occurrence of bird strikes. Taking Nanjing Lukou International Airport in China as an example, based on the DNA barcoding technology and detailed field research, we establish the most commonly struck species, which can help managers identify the level of hazard and lead to meaningful reductions in hazards and costs associated with bird strike. The investigation of bird communities showed that there were 149 bird species recorded within an 8 km radius. There were 89, 88, 61, and 88 species in the woodland, wetland, farmland, and urban area, respectively. In total, 303 samples identified 82 species representing 13 orders and 32 family of birds from bird strike cases, of which 24 species were not found in the field survey. Passeriformes were the most common order of birds identified, with 43 species represented in 167 identifications. Skylark, Thrush, Shrike, Lapwing, and Swallow were most likely to cause damage or substantial damage to aircraft when strikes occurred. In addition to birds, we identified 69 bats individuals (accounting for 22.77%) using DNA barcoding. The Bray-Curtis similarity analysis revealed that species involved in bird strike had the highest similarity with urban area. Our findings suggest that policymakers should pay more attention to managing the wetlands and urban areas surrounding the airport. These findings imply that DNA barcoding can add to the environmental monitoring in airports, which can facilitate hazard management and improve air safety.

The role of landscape in shaping bird community and implications for landscape management at Nanjing Lukou International Airport.

Understanding the patterns of bird diversity and its driving force is necessary for bird strike prevention. In this study, we investigated the effects of landscape on phylogenetic and functional diversity of bird communities at Nanjing Lukou International Airport (NLIA). Bird identifications and counting of individuals were carried out from November 2017 to October 2019. Based on the land-cover data, the landscape was divided into four main types, including farmlands, woodlands, wetlands, and urban areas. Bird phylogenetic and functional diversity were strongly affected by landscape matrix types. Species richness and Faith's phylogenetic distance were highest in woodlands, while mean pairwise distance (MPD), mean nearest-taxon distance (MNTD), and functional dispersion (FDis) were highest in wetlands. Based on the feeding behavior, carnivorous birds had the lowest species richness but had the highest FDis, which implied that carnivorous birds occupied most niches at the NLIA. Moreover, bird assemblages exhibited phylogenetic and functional clustering in the four kinds of landscapes. A variety of landscape attributes had significant effects on species diversity, phylogenetic and functional diversity. Landscape-scale factors played an important role in the shaping of bird communities around NLIA. Our results suggest that landscape management surrounding airports can provide new approaches for policymakers to mitigate wildlife strikes.

Taxonomic Status and Phylogenetic Relationship of the Charadriidae Family Based on Complete Mitogenomes.

Background: The Charadriiformes provide a good source for researching evolution owing to their diverse distribution, behavior, morphology, and ecology. However, in the Charadrii, family-level relationships remain understudied, and the monophyly of Charadriidae is also a subject of controversy. Methods: In the present study, we generated complete mitogenomes for two species, Charadrius leschenaultii and Charadrius mongolus, which were found to be 16,905 bp and 16,844 bp in length, respectively. Among the 13 protein codon genes, we observed variation in the rate of non-synonymous substitution rates, with the slowest rate found in COI and the fastest rate observed in ATP8. The Ka/Ks ratio for all Charadriidae species was significantly lower than one, which inferred that the protein-coding genes underwent purifying selection. Results: Phylogenetic analysis based on the genes of Cyt b, 12S and ND2 revealed that the genus Pluvialis is the sister group of three families (Haematopodidae, Ibidorhynchidae, Recurvirostridae). However, the phylogenetic analysis based on complete mitogenomes indicated that the genus Pluvialis is within the Charadriidae family. Conclusion: This study highlights the importance of carefully selecting the number of genes used to obtain accurate estimates of the species tree. It also suggests that relying on partial mtDNA genes with fast-evolving rates may lead to misleading results when resolving the Pluvialis sister group. Future research should focus on sequencing more mitogenomes at different taxonomic levels to gain a better understanding of the features and phylogenetic relationships within the Charadriiformes order.

Comparative Mitogenomics of True Frogs (Ranidae, Anura), and Its Implications for the Phylogeny and Evolutionary History of Rana.

The true frogs of the genus Rana are a complex and diverse group, containing approximately 60 species with wide distribution across Eurasia and the Americas. Recently, many new species have been discovered with the help of molecular markers and morphological traits. However, the evolutionary history in Rana was not well understood and might be limited by the absence of mitogenome information. In this study, we sequenced and annotated the complete mitochondrial genome of R. longicrus and R. zhenhaiensis, containing 22 tRNAs, 13 protein-coding genes, two ribosomal RNAs, and a non-coding region, with 17,502 bp and 18,006 bp in length, respectively. In 13 protein codon genes, the COI was the most conserved, and ATP8 had a fast rate of evolution. The Ka/Ks ratio analysis among Rana indicated the protein-coding genes were suffering purify selection. There were three kinds of gene arrangement patterns found. The mitochondrial gene arrangement was not related to species diversification, and several independent shifts happened in evolutionary history. Climate fluctuation and environmental change may have played an essential role in species diversification in Rana. This study provides mitochondrial genetic information, improving our understanding of mitogenomic structure and evolution, and recognizes the phylogenetic relationship and taxonomy among Rana.

Five new mitogenomes sequences of Calidridine sandpipers (Aves: Charadriiformes) and comparative mitogenomics of genus Calidris.

Background: The genus Calidris (Charadriiformes, Scolopacidae) includes shorebirds known as dunlin, knots, and sanderlings. The relationships between species nested within Calidris, including Eurynorynchus, Limicola and Aphriza, are not well-resolved. Methods: Samples were collected from Xiaoyangkou, Rudong County, Jiangsu Province, China. Mitogenomes were sequenced using the Illumina Novaseq 6000 platform for PE 2 × 150 bp sequencing, and then checked for PCR products. Protein-coding genes were determined using an Open Reading Frame Finder. tRNAscan-SE, MITOS, and ARWEN were used to confirm tRNA and rRNA annotations. Bioinformatic analyses were conducted using DnaSP 5.1 and MEGA X. Phylogenic trees were constructed using maximum likelihood and Bayesian analyses. Results: We sequenced and annotated the mitogenome of five species and obtained four complete mitogenomes and one nearly complete mitogenome. Circular mitogenomes displayed moderate size variation, with a mean length of 16,747 bp, ranging from 16,642 to 16,791 bp. The mitogenome encoded a control region and a typical set of 37 genes containing two rRNA genes, 13 protein-coding genes, and 22 tRNA genes. There were four start codons, four stop codons, and one incomplete stop codon (T-). The nucleotide composition was consistently AT-biased. The average uncorrected pairwise distances revealed heterogeneity in the evolutionary rate for each gene; the COIII had a slow evolutionary rate, whereas the ATP8 gene had a fast rate. dN/dS analysis indicated that the protein-coding genes were under purifying selection. The genetic distances between species showed that the greatest genetic distance was between Eurynorhynchus pygmeus and Limicola falcinellus (22.5%), and the shortest was between E. pygmeus and Calidris ruficollis (12.8%). Phylogenetic trees revealed that Calidris is not a monophyletic genus, as species from the genera Eurynorynchus and Limicola were nested within Calidris. The molecular data obtained in this study are valuable for research on the taxonomy, population genetics, and evolution of birds in the genus Calidris.

The complete mitogenome of scaly thrush Zoothera aurea (Passeriformes, Turdidae).

The complete mitochondrial genome of scaly thrush Zoothera aurea was obtained by next-generation sequencing. The circular genome was 16,712 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a control region. The overall nucleotide composition was A: 29.67%, T: 23.32%, C: 32.21%, and G: 14.80%. Nine genes were encoded on the light strand, and the remaining 28 genes were encoded on the heavy strand. Most of the PCGs began with the ATG as the start codon, and six kinds of termination codons were used in this mitogenome. This study improves our understanding of the mitogenomic characteristics and its phylogenetic relationships within Turdidae.